10 Jun 2019

RNAcentral release 12

We are pleased to announce that a new RNAcentral release is now available. Version 12 includes human lncRNAs from LncBook, >3 million rRNA secondary structures displayed in standard layouts, improved feature viewer, homology information from Ensembl Compara, and lots more.

Displaying secondary structure in standard orientations

In addition to the secondary structures (2Ds) provided by Expert Databases, such as GtRNAdb, RNAcentral now also displays 2D visualisations for >3 million rRNA sequences using the auto-traveler software that automatically generates the diagrams in standard layouts (manuscript in preparation). 

These familiar layouts enable comparison between structures and show the differences relative to the template. For example, in the following Thermus thermophilus small ribosomal subunit structure nucleotides in black are unchanged compared to the CRW template and the differences are shown in different colours:

At this time only SSU and 5S rRNA are supported (work on visualising other RNA types is underway). We would like to thank Dr David Hoksza for the help with the Traveler software and the Gutell lab for providing the rRNA templates. For more details, see the help centre or browse the sequences in RNAcentral.

LncBook joins RNAcentral

LncBook is a comprehensive resource of human lncRNAs featuring functional information, disease associations, expression information and more. With the addition of LncBook, RNAcentral now has 32 expert databases. We would like to thank Dr Lina Ma for help with importing these data. Browse RNAs from LncBook

Displaying orthologs and paralogs using Ensembl Compara

We implemented a new section of the sequence report pages that shows related RNA sequences identified by Ensembl Compara. For example, here is the hsa-mir-31 page displaying related sequences from 88 other species retrieved from Ensembl Compara:

Currently this functionality is limited to certain RNA types because the Compara pipeline analyses only RNAs from certain Rfam families. We are investigating ways of expanding these annotations in the future.

Improved feature viewer

Our feature viewer now displays the locations of mature miRNAs along side the Rfam annotations, modified nucleotides and conserved RNA structures. For example: the hsa-mir-3689b precursor shows the 5’ (URS000075D33D/9606) and 3’ (URS000075BB55/9606) mature miRNA products.

Thanks to Dr Sam Griffiths-Jones of miRBase for providing these annotations. We plan to continue to adding informative features to the viewer, so get in contact if you would like to submit your data.

Data updates

The following database have also been updated:
  • ENA (139)
  • Ensembl (96)
  • FlyBase (FB2019_02)
  • HGNC
  • PDB
  • RefSeq
  • Rfam (14.1)
  • TAIR
  • PomBase
  • WormBase (WS270)

Get in touch

The data are available on the RNAcentral website, via the API, and in the FTP archive. We plan to make the next release available in October 2019. In the meantime, if you have any feedback please feel free to get in touch by email, on Twitter, or by submitting an issue on GitHub. We look forward to hearing from you!